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Zinc in PDB 5wau: Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K

Enzymatic activity of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K

All present enzymatic activity of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K:
1.9.3.1;

Protein crystallography data

The structure of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K, PDB code: 5wau was solved by R.Fromme, I.Ishigami, S.Y.Yeh, N.Zatsepin, T.Grant, P.Fromme, D.Rousseau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 177.923, 182.555, 208.450, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 24.4

Other elements in 5wau:

The structure of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 4 atoms
Copper (Cu) 6 atoms
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K (pdb code 5wau). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K, PDB code: 5wau:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5wau

Go back to Zinc Binding Sites List in 5wau
Zinc binding site 1 out of 2 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:33.4
occ:1.00
 SG F:CYS82 2.3 33.2 1.0
SG F:CYS60 2.3 33.8 1.0
SG F:CYS85 2.3 34.4 1.0
SG F:CYS62 2.3 35.8 1.0
CB F:CYS82 3.2 33.5 1.0
CB F:CYS60 3.3 31.5 1.0
CB F:CYS85 3.3 31.2 1.0
CB F:CYS62 3.4 35.8 1.0
CA F:CYS62 3.6 38.4 1.0
N F:CYS85 3.8 32.2 1.0
N F:CYS62 4.0 36.5 1.0
CA F:CYS85 4.1 33.0 1.0
O F:CYS60 4.4 30.7 1.0
CB F:SER84 4.4 32.3 1.0
C F:CYS60 4.5 31.9 1.0
CA F:CYS60 4.5 30.5 1.0
OG F:SER84 4.7 35.1 1.0
CA F:CYS82 4.7 34.2 1.0
OG1 F:THR87 4.7 49.7 1.0
C F:CYS85 4.8 33.3 1.0
C F:SER84 4.8 32.7 1.0
C F:ILE61 4.9 35.7 1.0
N F:GLY86 4.9 36.6 1.0
C F:CYS62 4.9 40.1 1.0
CA F:SER84 5.0 32.7 1.0

Zinc binding site 2 out of 2 in 5wau

Go back to Zinc Binding Sites List in 5wau
Zinc binding site 2 out of 2 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Zn101

b:41.9
occ:1.00
 SG f:CYS85 2.3 42.6 1.0
SG f:CYS82 2.3 38.6 1.0
SG f:CYS62 2.3 43.3 1.0
SG f:CYS60 2.4 42.9 1.0
CB f:CYS82 3.2 37.0 1.0
CB f:CYS85 3.3 41.8 1.0
CB f:CYS60 3.3 38.2 1.0
CB f:CYS62 3.3 43.2 1.0
CA f:CYS62 3.6 43.5 1.0
N f:CYS85 3.7 41.1 1.0
CA f:CYS85 4.0 40.1 1.0
N f:CYS62 4.1 42.4 1.0
CG2 f:THR87 4.3 49.3 1.0
CB f:SER84 4.4 42.5 1.0
C f:CYS60 4.5 39.8 1.0
CA f:CYS60 4.5 39.0 1.0
O f:CYS60 4.5 37.7 1.0
O f:HOH209 4.5 55.7 1.0
CA f:CYS82 4.7 38.6 1.0
OG f:SER84 4.7 43.6 1.0
C f:SER84 4.7 40.7 1.0
C f:CYS85 4.8 37.3 1.0
C f:ILE61 4.9 40.3 1.0
N f:GLY86 4.9 40.4 1.0
CA f:SER84 5.0 41.7 1.0
N f:SER84 5.0 44.7 1.0
CB f:ILE70 5.0 36.4 1.0
CG1 f:ILE70 5.0 35.9 1.0
C f:CYS62 5.0 43.9 1.0

Reference:

I.Ishigami, N.A.Zatsepin, M.Hikita, C.E.Conrad, G.Nelson, J.D.Coe, S.Basu, T.D.Grant, M.H.Seaberg, R.G.Sierra, M.S.Hunter, P.Fromme, R.Fromme, S.R.Yeh, D.L.Rousseau. Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature. Proc. Natl. Acad. Sci. V. 114 8011 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28698372
DOI: 10.1073/PNAS.1705628114
Page generated: Mon Oct 28 14:01:43 2024

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